methylclockData: epigenetic clock coefficients and reference data for the methylclock R/Bioconductor package

These are the data resources used by the methylclock R/Bioconductor package to estimate epigenetic age from DNA methylation. They are the 28 resources added for the clocks introduced in the redesign of the package; the resources published earlier remain available through ExperimentHub. This deposit is the hosting location for those resources: the methylclockData package retrieves them from here through ExperimentHub. They are of no use on their own, and they are not new data. Every one of them was published by the authors of the corresponding clock, and this deposit only makes them retrievable in a stable, citable form. Contents 25 tables of clock coefficients or CpG sets, as R data files (.rda) 1 vector of CpG identifiers giving the input order of the AltumAge network 1 table of reference probe means used to normalize the DunedinPACE input 1 set of neural network weights and input scaler (.hdf5) Licences Each resource keeps the licence of its original source. They are not uniform, so this deposit is not offered under a single licence. In particular, coefDunedinPACE.rda and coefDunedinPACEGS.rda are covered by GPL-3 together with a non-commercial use restriction from TruDiagnostic; see the DunedinPACE repository for their terms. Anyone using these files is responsible for complying with the licence of each one. Resources File Contents Size Original source Licence coefDunedinPACE.rda Coefficients DunedinPACE pace-of-aging estimator 174x3 github.com/danbelsky/DunedinPACE GPL-3.0 plus a non-commercial restriction from TruDiagnostic coefDunedinPACEGS.rda DunedinPACE reference means for probe normalization 20000x2 github.com/danbelsky/DunedinPACE GPL-3.0 plus a non-commercial restriction from TruDiagnostic coefNEOaPMA450K.rda Coefficients NEOage post-menstrual age clock (450K) 410x2 doi.org/10.18632/aging.203637 See original publication coefNEOaPMAEPIC.rda Coefficients NEOage post-menstrual age clock (EPIC) 523x2 doi.org/10.18632/aging.203637 See original publication coefNEOaPNA450K.rda Coefficients NEOage post-natal age clock (450K) 304x2 doi.org/10.18632/aging.203637 See original publication coefNEOaPNAEPIC.rda Coefficients NEOage post-natal age clock (EPIC) 510x2 doi.org/10.18632/aging.203637 See original publication coefVidalBralo.rda Coefficients Vidal-Bralo blood clock 9x2 doi.org/10.3389/fgene.2016.00126 CC-BY-4.0 coefEpiTOC1.rda CpG set for the epiTOC1 mitotic counter 385x1 github.com/aet21/EpiMitClocks CC-BY-4.0 coefHypoClock.rda CpG set for the HypoClock solo-WCGW counter 678x1 github.com/aet21/EpiMitClocks CC-BY-4.0 coefStemTOC.rda CpG set for the stemTOC mitotic counter 371x1 github.com/aet21/EpiMitClocks CC-BY-4.0 coefCausAge.rda Coefficients CausAge causal clock 586x2 github.com/bio-learn/biolearn BSD-3-Clause coefDamAge.rda Coefficients DamAge damaging causal clock 1090x2 github.com/bio-learn/biolearn BSD-3-Clause coefAdaptAge.rda Coefficients AdaptAge adaptive causal clock 1000x2 github.com/bio-learn/biolearn BSD-3-Clause coefLin.rda Coefficients Lin blood clock 100x2 doi.org/10.18632/aging.100908 See original publication coefWeidner.rda Coefficients Weidner three-CpG clock 4x2 doi.org/10.1186/gb-2014-15-2-r24 See original publication coefAltumAgeRef.rda AltumAge input CpG order 20318 github.com/bio-learn/biolearn MIT coefAltumAge.hdf5 AltumAge neural network weights and scaler weights+scaler github.com/bio-learn/biolearn MIT coefMcCartneySmoking.rda Coefficients McCartney smoking EpiScore 233x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyAlcohol.rda Coefficients McCartney alcohol EpiScore 450x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyBMI.rda Coefficients McCartney body mass index EpiScore 1109x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyBodyFat.rda Coefficients McCartney body fat EpiScore 968x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyEducation.rda Coefficients McCartney education EpiScore 373x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyHDL.rda Coefficients McCartney HDL cholesterol EpiScore 737x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyLDL.rda Coefficients McCartney LDL cholesterol EpiScore 233x2 github.com/bio-learn/biolearn BSD-3-Clause coefMcCartneyTotalChol.rda Coefficients McCartney total cholesterol EpiScore 204x2 github.com/bio-learn/biolearn BSD-3-Clause coefRepliTali.rda Coefficients RepliTali mitotic clock 88x2 github.com/aet21/EpiMitClocks CC-BY-4.0 coefMcCigarette.rda Coefficients mCigarette smoking score 1255x2 github.com/aleksandra-chybowska/Smoking_EpiScore MIT coefEpiTOC2.rda Parameters for the epiTOC2 mitotic counter 163x3 github.com/aet21/EpiMitClocks CC-BY-4.0 Provenance The coefficients were obtained from the sources listed above and stored as R objects without altering their values, except for the AltumAge weights, which were converted from the PyTorch format published by biolearn into HDF5. Checksums for every file are published with the deposit. Related software methylclockData — the R package that serves these resources methylclock — the package that uses them to estimate epigenetic age